Category:FAQ

Contents

Better FAQ

Overview

Please post your FAQs here. I suggest you write a Q&A style list with a short answer. More involved answers should link to its own page. Just my suggestion. Should we have topics? Please note, not all AQ are FAQ. Also, many answers to frequently recurring problems are probably best sought by searching for your terms in the Wiki.

Installation

Q: I've installed PyMol_0_98, and recently my structures have stopped displaying. I've tried uninstalling PyMol_0_98 and installing PyMol_0_97, and yet i've ran into the same problem...my .pdb files no longer display, although it is evident that they are being loaded and I can edit them.

Does anybody have any clue as to what might be the problem?
Thanks, shebsmehr

Startup

Q: I've installed PyMol_0_98 correctly but I can't open my files in .mol2 or .pdb format from the menubar. Instead I can open them with the program. I can't even save the images I create in PyMol and obviously the mivie too.

Could you help me to solve these problems.
Thanks
Vittorio

A1: Vittorio, if I understand you correctly, then you need to (a) make sure you have the PDB file on your machine, say Desktop (or home directory, for *nix), then in the GUI click on, "File"->"Open" then use the dialog to find the file you want to load. You can save time if you know where the file is by just using PyMol's "load" command

A2: To save images you have a couple options. First, to save a quick raw screen dump type, "png fileName" to save a PNG image (IE and other programs can view these files). Or, secondly, if you prefer a higher quality image with ray-traced shadows and textures you can do, "ray" then, the above "png" command.

Hope this helps. If it didn't please restate your question to make it more clear.

Q: Hi I have a problem. For some reason PyMOl do not display certain areas (several loops) of my .pdb file (1DAN) when in cartoon. When I display the structure in "lines" or "sticks" everything is ok. Furthermore, other .pdb viewers dont have this problem. I have tried several things:
1. Upgraded to the newest version og PyMol.
2. Redefined secondary structure using the "alter command".
3. Imported the .pdb file into SwissViewer, saved as the imported structure as a .pdb file, and then imported into PyMOl.

None of these things have solved the problem. Help please! (I would hate to have to start using another pdb-viewer!!)
Cheers
Kasper

Q: What I should write into the .pymolrc (Mandriva Linux) to be able open PyMol with .pdb or .pml from shell? I was able to run pymol *.pdb with old 0.99rc6 version, but then I upgraded Mandriva Linux and this option is not working anymore.

Settings

Q: I am wondering how to change the default settings for a color "spectrum". I would like to color by b-factor but not with the default spectrum but from white-to-red.

Q: I would like the distance labels generated with the 'distance' command to be single-digit only, e.g. 2.8 instead of 2.77. How can I do this? Thanks, MindFrog

A: Setting startup settings and python commands can be done in a file: ~/.pymolrc
E.g. command in there: cmd.set('label_distance_digits',1)
On my windows machine this is in C:\Documents and Settings\jurgen.WHELK.000\.pymolrc

Commands

Q: I want to move one object while keeping another fixed. How do I do this?

A: Load the proteins as separate objects, put the mouse into 3-button editing mode, then shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. (Warren DeLano answer)

Q: I'd like to select residues that are in contact with a surface, or else be able to select buried/non-buried residues, is there any way to do this ? Xevi 03:52, 16 Jun 2006 (CDT)

I'm also looking for this (e.g. to see available lysines' -NH2 or cysteines' -SH on the surface), could one maybe cover the protein with an additional layer of new atoms, and then select all protein atoms close to these? Edit: there is now a simple solution for proteins displayed as non-transparent surfaces: Displaying_Biochemical_Properties#Residues_with_functional_groups -- moino 19:35, 7 October 2008 (CDT)

Q: After using the usual mset command to rotate an object, states/frames are loaded into that object. However, using the "frame" command has odd behaviour (in comparison to loading a molecular dynamics trajectory into the state in which the "frame" command behaves normally). Can anyone explain this?

See MovieSchool for more help. There, frames, states and scenes are more clearly defined.

Q: How do I suppress the 'ExecutiveRMS' output while running cmd.pair_fit()?

Q: How does cmd.rms() choose a mapping between atoms in the selections? Exhaustive search over all possibilities?

Q: How do I select (especially, iterate through a set of) bonds? The existence of cycle valence seems to imply that it can be done. Is this possible via the API?

Q: I am doing some MD simulations using CHARMM (not AMBER) and would like to visualize the .dcd files output by CHARMM. I understand that PyMol can open .trj files from AMBER but is there a way to open up these .dcd files and if not, are there any plans to implement this? Thank you for your time!

Others

Q: I was wondering what the percentage given under the mutengensis wizard means? Thanks...

Q: Some of the bases in RNA helices are missing (not all in any given helix) when I am showing them in the CARTOON mode. How should I set it to get them shown? I tried the Secondary Structure Assignment commands, they did not work.

Q: Why does PyMol run version 2.3 of Python when I have Python 2.5 installed? How do I tell it to switch?

A: PyMOL runs on the older version of Python because it is known to work with the given feature set. You can easily upgrade to Python2.4--Python2.6 with newer PYMOLs, or you can run any version of Python by compiling your own source.

Q: How do I cite PyMOL?

A: Up-to-date citation formats, including downloadable BibTex and EndNote files can be found on PyMOL's Citation page, http://pymol.org/citing.

Q: What is the status of the VMD plugin for Pymol? How does one install it? Is it installed by default? Will it appear in the plugins list? I compiled from source and changed several configuration files, but I cant't seem to be able to get the VMD plugins working properly. Thanks!

Q: If I want to ask a question to the PyMol Wiki community, how do I do that? Is there a page for PyMol usage questions?

A: That's a very good question. I will try to find a local 'forum' or page or something like that for discussion.